7YRG: Histone methyltransferase

histone methyltransferase. Determined by electron microscopy at 4.2 Å resolution. Released 13 Dec 2023.

Method: Electron microscopy
Resolution: 4.2 Å
Organisms: Xenopus laevis, Homo sapiens
Chains: 12
Atoms: 16,377
Mol. weight: 247.49 kDa
Ligands: SAM, ZN
Released: 13 Dec 2023

Explore 7YRG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YRG contains 57 α-helices and 48 β-strands across 10 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	97-98	2	3

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	19-22	4
α-helix	29-37	9
β-strand	45-46	2	4
α-helix	48-76	29
β-strand	80-81	2	5
α-helix	83-92	10
α-helix	94-99	6
β-strand	103-104	2	6

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	32-34	3
α-helix	38-48	11
β-strand	53-54	2	5
α-helix	56-83	28
β-strand	88-89	2	4
α-helix	91-101	11
α-helix	105-122	18

Chain E: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	36-38	3
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	7
α-helix	86-113	28
α-helix	121-131	11

Chain F: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	97-98	2	6

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	19-22	4
α-helix	29-36	8
β-strand	45-46	2	8
α-helix	48-75	28
β-strand	80-81	2	9
α-helix	83-92	10
α-helix	94-99	6
β-strand	103-104	2	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	9
α-helix	56-83	28
β-strand	88-89	2	8
α-helix	91-101	11
α-helix	105-122	18

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.2	A, E	protein	103	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	102	Xenopus laevis	P62799 (AlphaFold model)
DNA (146-mer)	I, J	DNA	146	Homo sapiens
Histone H2A.Z	C, G	protein	113	Homo sapiens	P0C0S5 (AlphaFold model)
Histone H2B 1.1	D, H	protein	95	Xenopus laevis	P02281 (AlphaFold model)
[histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B	K, L	protein	279	Homo sapiens	Q4FZB7

Sequence of entity 1 (A, E), FASTA

>7YRG_1 Histone H3.2 (chains A, E)
GEVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMAL
QEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>7YRG_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRXVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (I, J), FASTA

>7YRG_3 DNA (146-MER) (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT

Sequence of entity 4 (C, G), FASTA

>7YRG_4 Histone H2A.Z (chains C, G)
GKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELA
GNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKSLIGKKG

Sequence of entity 5 (D, H), FASTA

>7YRG_5 Histone H2B 1.1 (chains D, H)
KTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Sequence of entity 6 (K, L), FASTA

>7YRG_6 [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B (chains K, L)
GQSRYVPSSGMSAKELCENDDLATSLVLDPYLGFQTHKMNTRFRPIKGRQEELKEVIERF
KKDEHLEKAFKCLTSGEWARHYFLNKNKMQEKLFKEHVFIYLRMFATDSGFEILPCNRYS
SEQNGAKIVATKEWKRNDKIELLVGCIAELSEIEENMLLRHGENDFSVMYSTRKNCAQLW
LGPAAFINHDCRPNCKFVSTGRDTACVKALRDIEPGEEISCYYGDGFFGENNEFCECYTC
ERRGTGAFKSRVGLPAPAPVINSKYGLRETDKRLNRLKK

Ligands and cofactors

ID	Name	Formula	Copies
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	2
ZN	Zinc ion	Zn	2

Primary citation

Structural insight into H4K20 methylation on H2A.Z-nucleosome by SUV420H1. Huang, L., Wang, Y., Long, H. et al. Mol Cell (2023) 83:2884-2895.e7. DOI 10.1016/j.molcel.2023.07.001 · PubMed

Other PDB entries of the same protein (UniProt P84233 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
3GV6 1.76 Å, Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
4QEO 2.0 Å, crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH
1S32 2.05 Å, Molecular Recognition of the Nucleosomal 'Supergroove'
3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome

Browse structure collections

About this viewer

MolViewer shows 7YRG directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.